genoml-train

Usage:
  genoml-train (--model-file=model_file|--model-dir=model_dir) (--geno-prefix=geno_prefix) (--pheno-file=<pheno_file>) [--addit-file=<addit_file>] [--cov-file=<cov_file>] [--cv-reps=<cv_reps>] [--grid-search=<grid_search>] [--gwas-file=<gwas_file>] [--herit=<herit>] [--impute-data=<impute_data>] [--n-cores=<n_cores>] [--train-speed=<train_speed>] [--no-tune] [-v | -vv | -vvv]
  genoml-train -h | --help
  genoml-train --version

Options:
  --model-file=model_file                 Path to the model file to save.
  --model-dir=model_dir                   Path to a directory to store the model.
  --geno-prefix=geno_prefix               Prefix with path to genotype files in PLINK format, *.bed, *.bim and *.fam.
  --pheno-file=<pheno_file>               Path to the phenotype file in PLINK format, *.pheno.
  --gwas-file=<gwas_file>                 Path to the GWAS file, if available.
  --cov-file=<cov_file>                   Path to the covariance file, if available.
  --herit=<herit>                         Heritability estimate of phenotype between 0 and 1, if available.
  --addit-file=<addit_file>               Path to the additional file, if avialable.
  --n-cores=<n_cores>                     Number of cores to be allocated for computation [default: 1].
  --train-speed=<train_speed>             Training speed: (ALL, FAST, FURIOUS, BOOSTED). Run all models, only  the fastest models, run slightly slower models, or just run boosted models which usually perform best when using genotype data [default: BOOSTED].
  --cv-reps=<cv_reps>                     Number of cross-validation. An integer greater than 5. Effects the speed [default: 5].
  --impute-data=<impute_data>             Imputation: (knn, median). Governs secondary imputation and data transformation [default: median].
  --grid-search=<grid_search>             Grid search length for parameters, integer greater than 10, 30 or greater recommended, effects speed of initial tune [default: 10].
  --no-tune                               Disable Tuning. This reduces the accuracy of the trained model but significately increases the training time.
  -v -vv -vvv                             Verbose output.
  -h --help                               Show this screen.
  --version                               Show version.

Examples:
  genoml-train --model-file=model.genoml_model --geno-prefix=./exampleData/example --pheno-file=./exampleData/training.pheno --gwas-file=./exampleData/example_GWAS.txt

Help:
  For help using this tool, please open an issue on the Github repository:
  https://github.com/GenoML/genoml-train-core/issues
